1 #ifndef DECONVOLUTECOMMAND_H
2 #define DECONVOLUTECOMMAND_H
7 * Created by Sarah Westcott on 1/21/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
15 /* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
16 containing 2 columns. The first being the groupname and the second the list of identical sequence names. */
19 class DeconvoluteCommand : public Command {
22 DeconvoluteCommand(string);
24 ~DeconvoluteCommand() {}
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 string inFastaName, oldNameMapFName, outputDir;
34 vector<string> outputNames;
35 map<string, vector<string> > outputTypes;